Note: For some reason Oracle no longer seems to use 1 bundle patch for both Oracle SOA 12.1.3 & BPM 12.1.3
The 12.1.3.0.3 patches 20900599 (SOA) and 20645340 (BPM) are also conflicting according to OPatch.
So you can either patch your environment (server runtime or local JDev) for BPM or SOA.

So (again) I patched my own JDeveloper 12.1.3 environment with the OPATCH tool.Extract the downloaded patch, I’ll use C:\temp\p20645340_121300_Generic\20645340
This folder is called ‘patch_TOP’ in opatch terminology.

Since I use Windows as local OS you will need to First open a command prompt with Administrator rights (right-click, run as Administrator).
If we don’t use the right permissions we will get the error: Unable to lock Central Inventory. OPatch will attempt to re-lock

First we set our ORACLE_HOME to the Jdeveloper 12.1.3 folder:
SET ORACLE_HOME=C:\ORACLE\middleware\12.1.3
And make sure opatch is in our path:
SET PATH=%PATH%;C:\ORACLE\middleware\12.1.3\OPatch
We browse to the patch_top folder:
cd C:\temp\p20645340_121300_Generic\20645340
And run opatch:
opatch apply